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. 2021 Nov 24;6(12):1549–1560. doi: 10.1038/s41564-021-01000-z

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© The Author(s) 2021

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Extended Data Fig. 4 — A- Recombination masked WGS phylogeny, showing the Nichols-lineage and sublineages. Shaded grey box shows a monophyletic clade containing commonly used reference genomes as well as genetically related strains. Tip points are coloured by sublineage, and coloured strips show sublineage and country. Pink triangle indicates collapsed SS14-lineage. B- Expanded view of a seemingly extinct clade containing common reference strains including Nichols_v2, DAL-1 and Seattle_Nichols. The most recent sample closely related to the reference strains (TPA_USL-SEA-83-1) was collected in 1983, while the latest sample for the entire clade (TPA_USL-Phil-3) was collected in 1987. The provenance of the sample originally used for sequencing the DAL-1 genome is uncertain, but in the literature the original isolation was in 1988. The placement of both DAL-1 and TPA_USL-SEA-83-1 within the diversity of Nichols-1912 derivatives suggests the possibility of the samples being mislabeled in the handling laboratories.